MolNFT v1 · #137264 · protein
Ferredoxin NADP oxidoreductase (xfn)
5VJ7: “Ferredoxin NADP oxidoreductase (xfn)”. X-ray diffraction, 4 ligands (SF4, FAD, FES), 8 pockets (best druggability 0.83). MolNFT v1 #137264 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VJ7
- Type
- protein
- Length
- 744 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase; Ferredoxin-NADP(+) reductase subunit alpha
- EC
- 1.18.1.2
- UniProt
- I6V148, I6TYZ3
- Ligands
- SF4, FAD, FES, MG
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase | protein | 462 | 39% helix, 18% strand | I6V148 |
| B | Ferredoxin-NADP(+) reductase subunit alpha (EC 1.18.1.2) | protein | 282 | 27% helix, 30% strand | I6TYZ3 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- FES · Fe2/s2 (inorganic) cluster · ligand · chains B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.83 | 0.86 | 105 | FAD |
| 2 | 848 | 0.80 | 0.83 | 73 | FAD, MG |
| 3 | 51 | 0.64 | 0.95 | 16 | empty |
| 4 | 112 | 0.47 | 0.80 | 26 | empty |
| 5 | 150 | 0.45 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2020 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 5VJ7 · Ferredoxin NADP Oxidoreductase (Xfn) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt I6V148
- Every structure of UniProt I6TYZ3
- Elsewhere: RCSB PDB 5VJ7 · PDBe 5VJ7 · UniProt I6V148 · UniProt I6TYZ3
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